I don't think Insane in the Membrane or Hun on the Run should be considered Turtle-centric episodes at all; they're Stockman and Hun-focused episodes. The Turtles are just bit players in them. Bishop's Gambit also largely revolves around Bishop's work engineering a faux alien invasion, but it does feature the Turtles more heavily.

Wish we'd gotten more villain-centric episodes, I'd have loved more episodes focused on Hun, Stockman, and Bishop. Though I enjoyed Hun and Stockman's uneasy partnership in season three when both of them were on Shredder's ****-list.